7/18/2018

Raw centroids

  • median value of markers in each cluster

Normalized centroids

  • median z-score of markers in each cluster

Freq cluster

  • median z-score of markers in each cluster

Freq population

  • median z-score of markers in each cluster

Meta Phenograph +Meta tsne

##   Running PhenoGraph...  Finding nearest neighbors...DONE ~ 0.105 s
##   Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 1.376 s
##   Build undirected graph from the weighted links...DONE ~ 0.229 s
##   Run louvain clustering on the graph ...DONE ~ 0.097 s
##   Return a community class
##   -Modularity value: 0.8954807 
##   -Number of clusters: 16 DONE!
##   Running t-SNE...with seed 42  DONE
  • colored by “meta” phenograph cluster

Meta Phenograph +Meta tsne

  • colored by control

Meta Phenograph +Meta tsne

  • colored by control

Meta Phenograph +Meta tsne

  • colored by percent of cells that are naive in original clusters
  • keep slide 4 in mind

Meta Phenograph +Meta tsne

  • colored by percent of cells that are effector in original clusters

Meta Phenograph +Meta tsne

  • colored by percent of cells that are effector memory in original clusters

Meta Phenograph +Meta tsne

  • colored by percent of cells that are central memory in original clusters

Meta Phenograph +Meta tsne

  • colored by median CD45 (scaled) expression in original clusters

Meta Phenograph +Meta tsne

  • colored by median CCR7 (scaled) expression in original clusters

Meta Phenograph +Meta tsne

  • colored by median CD28 (scaled) expression in original clusters

Meta Phenograph +Meta tsne

  • colored by median CD95 (scaled) expression in original clusters

Meta Phenograph +Meta tsne

  • colored by median CD27 (scaled) expression in original clusters
## 
## FALSE  TRUE 
##    67    12

Meta Phenograph +Meta tsne

  • meta-clusters 14, 3, 2